RNA sequencing: new technologies and applications in cancer research

M Hong, S Tao, L Zhang, LT Diao, X Huang… - Journal of hematology & …, 2020 - Springer
Over the past few decades, RNA sequencing has significantly progressed, becoming a
paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing …

Bibliometric review of ATAC-Seq and its application in gene expression

L Luo, M Gribskov, S Wang - Briefings in Bioinformatics, 2022 - academic.oup.com
With recent advances in high-throughput next-generation sequencing, it is possible to
describe the regulation and expression of genes at multiple levels. An assay for transposase …

Loss of gene information: Discrepancies between RNA sequencing, cDNA microarray, and qRT-PCR

N Rachinger, S Fischer, I Böhme… - International Journal of …, 2021 - mdpi.com
Molecular analyses of normal and diseased cells give insight into changes in gene
expression and help in understanding the background of pathophysiological processes …

A statistical simulator scDesign for rational scRNA-seq experimental design

WV Li, JJ Li - Bioinformatics, 2019 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) has revolutionized biological sciences
by revealing genome-wide gene expression levels within individual cells. However, a critical …

Going the distance: optimizing RNA-Seq strategies for transcriptomic analysis of complex viral genomes

DP Depledge, I Mohr, AC Wilson - Journal of virology, 2019 - Am Soc Microbiol
Transcriptome profiling has become routine in studies of many biological processes.
However, the favored approaches such as short-read Illumina RNA sequencing are giving …

Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression …

Z Ahmed, EG Renart, S Zeeshan, XQ Dong - Human genomics, 2021 - Springer
Background Genetic disposition is considered critical for identifying subjects at high risk for
disease development. Investigating disease-causing and high and low expressed genes …

Processing and analysis of RNA-seq data from public resources

Y Zoabi, N Shomron - Deep Sequencing Data Analysis, 2021 - Springer
Advances in next generation sequencing (NGS) technologies resulted in a broad array of
large-scale gene expression studies and an unprecedented volume of whole messenger …

Bioinformatics analysis reveals potential biomarkers associated with the occurrence of intracranial aneurysms

C Zhao, Z Ma, J Shang, X Cui, J Liu, R Shi, S Wang… - Scientific Reports, 2022 - nature.com
To better understand the molecular mechanisms of intracranial aneurysm (IA) pathogenesis,
we used gene coexpression networks to identify hub genes and functional pathways …

Advancing brain barriers RNA sequencing: guidelines from experimental design to publication

DMF Francisco, L Marchetti… - Fluids and Barriers of …, 2020 - Springer
Abstract Background RNA sequencing (RNA-Seq) in its varied forms has become an
indispensable tool for analyzing differential gene expression and thus characterization of …

Strategy for RNA-seq experimental design and data analysis

G Gimenez, PA Stockwell, EJ Rodger… - Oral Biology: Molecular …, 2022 - Springer
Ribonucleic acids (RNAs) are fundamental molecules that control regulation and expression
of the genome and therefore the function of a cell. Robust analysis and quantification of RNA …